Quality Filters
The Quality Filters allow one to filter variants by variant quality metrics. The filter can operate in a Simple or Advanced mode.
Modes
Simple
Select a minimum degree of sequencing Quality (Low, Moderate, High).
Advanced
For SNVs and Indels:
Select a minimum degree of sequencing Quality (Low, Moderate, High),
Define minimum Mapping Quality (0-60 - value can be exceeded using the text box),
Specify minimum Depth (0-500 - value can be exceeded using the text box),
Set minimum number of alternate reads in Alternate Read (0-500 - value can be exceeded using the text box). Note: available for cases run with pipeline version 5.26+.
Set limits on Allele bias (0-100). Note: when applied to mtDNA variants, the Allele bias filter operates on heteroplasmy levels.
For CNVs:
Set limits on CNV Length (50bp, 1kb, 10kb, 100kb, 1Mb, 100Mb, Max CNV length),
Set minimum CNV Bin Count (1, 5, 10, 25, 50, 100, 500).
Default values
Quality: Moderate and High,
Mapping Quality ≥45,
Depth ≥ 10,
Alternate Read - no filtering,
Allele bias - no filtering,
CNV Length - no filtering,
CNV Bin Count - no filtering.
As of version 2.26:
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